Research Topics
| R J RobertsSummaryAffiliation: New England Biolabs Country: USA Publications
| Collaborators
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Detail Information
Publications
Genomic functional annotation using co-evolution profiles of gene clustersYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
Genome Biol 3:RESEARCH0060. 2002..We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles...- Identifying protein function--a call for community actionRichard J Roberts
New England Biolabs, located in Beverly, Massachusetts, USA
PLoS Biol 2:E42. 2004 - REBASE--restriction enzymes and DNA methyltransferasesRichard J Roberts
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915 USA
Nucleic Acids Res 33:D230-2. 2005..The contents of REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be requested via email... - REBASE--a database for DNA restriction and modification: enzymes, genes and genomesRichard J Roberts
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 38:D234-6. 2010..The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email... - The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifsRobert K Neely
School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
BMC Mol Biol 9:48. 2008..Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC... - A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance systemJonathan O'Driscoll
Department of Microbiology, University College Cork, Cork, Ireland
BMC Microbiol 6:40. 2006..LlaJI and R2.LlaJI). Here we employ a detailed genetic analysis of the LlaJI restriction determinants in an attempt to characterize mechanistic features of this unusual hetero-oligomeric endonuclease... - Phylogenetic detection of conserved gene clusters in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA, USA
BMC Bioinformatics 6:243. 2005.... - REBASE-restriction enzymes and methylasesR J Roberts
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 25:248-62. 1997..neb.com/rebase ). Specialized files are available that can be used directly by many software packages... - REBASE: restriction enzymes and methyltransferasesRichard J Roberts
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 31:418-20. 2003..The data is available on the web (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and as monthly updates via email... - How restriction enzymes became the workhorses of molecular biologyRichard J Roberts
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Proc Natl Acad Sci U S A 102:5905-8. 2005..This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted... - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genesRichard J Roberts
New England Biolabs, Beverly, MA 01915, USA
Nucleic Acids Res 31:1805-12. 2003..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes... - REBASE--enzymes and genes for DNA restriction and modificationRichard J Roberts
New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 35:D269-70. 2007..The contents or REBASE may be browsed from the web (http://rebase.neb.com/rebase/rebase.ftp.html) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email... - COMBREX: COMputational BRidge to EXperimentsRichard J Roberts
New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
Biochem Soc Trans 39:581-3. 2011..A pilot project is running that focuses on bacterial and archaeal genomes... - REBASE--restriction enzymes and methylasesR J Roberts
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 29:268-9. 2001..The data is distributed via email, ftp (ftp.neb.com) and the Web (http://rebase. neb.com)... - The early days of bioinformatics publishingR J Roberts
New England Biolabs, Beverly, MA 01915, USA
Bioinformatics 16:2-4. 2000..A brief history of the early days of publishing in the bioinformatics field is presented... - REBASE - restriction enzymes and methylasesR J Roberts
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 28:306-7. 2000..Most recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The data is distributed via Email, ftp (ftp.neb.com), and the Web (http://rebase.neb.com)... - REBASE-restriction enzymes and methylasesR J Roberts
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 27:312-3. 1999..Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages... - Base flippingR J Roberts
New England Biolabs, Beverly, Massachusetts 01915, USA
Annu Rev Biochem 67:181-98. 1998..This review describes systems known to use base flipping as well as many systems where it is likely to occur but has not yet been rigorously demonstrated. The mechanism and evolution of base flipping are also discussed... - REBASE - restriction enzymes and methylasesR J Roberts
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 26:338-50. 1998..Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages... - COMBREX: a project to accelerate the functional annotation of prokaryotic genomesRichard J Roberts
Bioinformatics Program, Boston University, Boston, MA 02215, USA
Nucleic Acids Res 39:D11-4. 2011..It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids... - Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genomeH Kong
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 28:3216-23. 2000..Helicobacter pylori may maintain a variety of functional R-M systems, which are believed to be a primitive bacterial 'immune' system, by alternatively turning on/off a subset of numerous R-M systems... - NEBcutter: A program to cleave DNA with restriction enzymesTamas Vincze
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 31:3688-91. 2003..Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini... - Segmentally variable genes: a new perspective on adaptationYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
PLoS Biol 2:E81. 2004..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment... - Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structureQian Steven Xu
Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
Protein Sci 14:2590-600. 2005..Combined with structural information from other solved structures of Type II restriction enzymes, the possible relationship between the structures of the enzymes and their cleavage behaviors is discussed... - DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferaseS Kumar
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 25:2773-83. 1997..This inhibitory effect can be partially overcome after a considerably long time in the crystal environment where the packing prevents complex dissociation and the target is accurately positioned within the active site... - Comparative genomics of the restriction-modification systems in Helicobacter pyloriL F Lin
New England Biolabs, Inc, 32 Tozer Road, Beverly, MA 01915, USA
Proc Natl Acad Sci U S A 98:2740-5. 2001..Our results also show that H. pylori has extremely diversified R-M systems in different strains, and that the diversity may be maintained by constantly acquiring new R-M systems and by inactivating and deleting the old ones... - Selection of restriction endonucleases using artificial cellsYu Zheng
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 35:e83. 2007..manalii. This method provides a unique tool for cloning restriction endonuclease genes and has many other potential applications... - Characterization of two new aminopeptidases in Escherichia coliYu Zheng
Bioinformatics Graduate Program, Boston University, Massachusetts 02215, USA
J Bacteriol 187:3671-7. 2005..ypdE is the immediate downstream gene of ypdF, and its start codon overlaps with the stop codon of ypdF by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity... - Identification of genes with fast-evolving regions in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
Nucleic Acids Res 32:6347-57. 2004..Gene sets reported from our method provide a measure of the phenotypic divergence between two closely related genomes... - A unique family of Mrr-like modification-dependent restriction endonucleasesYu Zheng
New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
Nucleic Acids Res 38:5527-34. 2010..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms... - Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilisBrian P Anton
New England Biolabs, Ipswich, MA 01938, USA
Nucleic Acids Res 38:6195-205. 2010..Finally, we performed a computational analysis to identify candidate residues outside the TRAM domain that may be involved with substrate recognition. These residues represent interesting targets for further analysis... - Computational identification of operons in microbial genomesYu Zheng
Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA
Genome Res 12:1221-30. 2002..We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution... - Using shotgun sequence data to find active restriction enzyme genesYu Zheng
New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
Nucleic Acids Res 37:e1. 2009..Active restriction enzyme genes have been identified, and their activity demonstrated biochemically, in the sequenced genomes of Methanocaldococcus jannaschii, Bacillus cereus ATCC 10987 and Methylococcus capsulatus... - RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coliBrian P Anton
New England Biolabs, Ipswich, MA 01938, USA
Proc Natl Acad Sci U S A 105:1826-31. 2008..The initial results presented here constitute a bioinformatics-driven prediction with preliminary experimental validation that should serve as the starting point for several interesting lines of further inquiry... - Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferasesGun Do Kim
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
EMBO J 21:4183-95. 2002..In vivo co-expression of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting co-operation between de novo and maintenance enzymes during DNA methylation... - The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNASophie Laget
New England Biolabs, Ipswich, Massachusetts, United States of America
PLoS ONE 5:e11982. 2010..It is unknown whether MBD5 or MBD6 also bind methylated DNA; this question has interest for basic research, but also practical consequences for human health, as MBD5 deletions are the likely cause of certain cases of mental retardation... - Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferaseS Pradhan
New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
Nucleic Acids Res 25:4666-73. 1997..The new clones are capable of yielding large quantities of intact MTases for further structural and functional studies... - Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspIZhe Yang
Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA
Nucleic Acids Res 33:1892-901. 2005..A possible functional link between this unusual dimerization mode and the tetrameric restriction enzymes is discussed... - DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansionJohn R Horton
Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA
Nucleic Acids Res 34:939-48. 2006.... - Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraintsMasha Y Niv
Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave, New York, New York 10021, USA
Proteins 71:631-40. 2008..The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering... - Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferaseZhe Yang
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
J Mol Biol 340:695-706. 2004..Comparative phylogenetic analysis of the hemK gene and its frequent neighbor gene, prfA, which encodes a major substrate, provides evidence for several examples of lateral gene transfer... - An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition siteQian Steven Xu
Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, MA 02118, USA
Structure 12:1741-7. 2004..A few possible pathways are discussed for MspI to cut both strands of DNA, either as a monomer or dimer... - Preserving an important collectionNorton Zinder
Science 307:519. 2005 - Save your notes, drafts and printouts: today's work is tomorrow's historySydney Brenner
Nature 446:725. 2007 - Richard J. Roberts--Nobel Laureate for discovery of split genesMarc A Shampo
Mayo Clin Proc 78:132. 2003 - Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactionsAiping Dong
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
Biol Chem 385:373-9. 2004..A possible evolutionary link between the Type I and Type II restriction-modification systems is discussed...